OpenRaiser/Intern-Atlas huggingface dataset:
Complex Tilings
Venue: arXiv cs.CC 2007
Year: 2007

We study the minimal complexity of tilings of a plane with a given tile set. We note that every tile set admits either no tiling or some tiling with O(n) Kolmogorov complexity of its n-by-n squares. We construct tile sets for which this bound is tight: all n-by-n squares in all tilings have complexity at least n. This adds a quantitative angle to classical results on non-recursivity of tilings -- that we also develop in terms of Turing degrees of unsolvability. Keywords: Tilings, Kolmogorov complexity, recursion theory
Indexing Schemes for Similarity Search In Datasets of Short Protein Fragments
Venue: arXiv cs.DS 2007
Year: 2007

We propose a family of very efficient hierarchical indexing schemes for ungapped, score matrix-based similarity search in large datasets of short (4-12 amino acid) protein fragments. This type of similarity search has importance in both providing a building block to more complex algorithms and for possible use in direct biological investigations where datasets are of the order of 60 million objects. Our scheme is based on the internal geometry of the amino acid alphabet and performs exceptionally well, for example outputting 100 nearest neighbours to any possible fragment of length 10 after scanning on average less than one per cent of the entire dataset.
Theoretical cryptanalysis of the Klimov-Shamir number generator TF-1
Venue: arXiv cs.CR 2007
Year: 2007

The internal state of the Klimov-Shamir number generator TF-1 consists of four words of size w bits each, whereas its intended strength is 2^{2w}. We exploit an asymmetry in its output function to show that the internal state can be recovered after having 2^w outputs, using 2^{1.5w} operations. For w=32 the attack is practical, but for their recommended w=64 it is only of theoretical interest.
On the number of t-ary trees with a given path length
Venue: arXiv cs.DM 2007
Year: 2007

We show that the number of $t$-ary trees with path length equal to $p$ is $\exp(h(t^{-1})t\log t \frac{p}{\log p}(1+o(1)))$, where $\entropy(x){=}{-}x\log x {-}(1{-}x)\log (1{-}x)$ is the binary entropy function. Besides its intrinsic combinatorial interest, the question recently arose in the context of information theory, where the number of $t$-ary trees with path length $p$ estimates the number of universal types, or, equivalently, the number of different possible Lempel-Ziv'78 dictionaries for sequences of length $p$ over an alphabet of size $t$.
Branch-and-Prune Search Strategies for Numerical Constraint Solving
Venue: arXiv cs.AI 2007
Year: 2007

When solving numerical constraints such as nonlinear equations and inequalities, solvers often exploit pruning techniques, which remove redundant value combinations from the domains of variables, at pruning steps. To find the complete solution set, most of these solvers alternate the pruning steps with branching steps, which split each problem into subproblems. This forms the so-called branch-and-prune framework, well known among the approaches for solving numerical constraints. The basic branch-and-prune search strategy that uses domain bisections in place of the branching steps is called the bisection search. In general, the bisection search works well in case (i) the solutions are isolated, but it can be improved further in case (ii) there are continuums of solutions (this often occurs when inequalities are involved). In this paper, we propose a new branch-and-prune search strategy along with several variants, which not only allow yielding better branching decisions in the latter case, but also work as well as the bisection search does in the former case. These new search algorithms enable us to employ various pruning techniques in the construction of inner and outer approximations of the solution set. Our experiments show that these algorithms speed up the solving process often by one order of magnitude or more when solving problems with continuums of solutions, while keeping the same performance as the bisection search when the solutions are isolated.
On the Axiomatisation of Boolean Categories with and without Medial
Venue: arXiv cs.LO 2007
Year: 2007

The term ``Boolean category'' should be used for describing an object that is to categories what a Boolean algebra is to posets. More specifically, a Boolean category should provide the abstract algebraic structure underlying the proofs in Boolean Logic, in the same sense as a Cartesian closed category captures the proofs in intuitionistic logic and a *-autonomous category captures the proofs in linear logic. However, recent work has shown that there is no canonical axiomatisation of a Boolean category. In this work, we will see a series (with increasing strength) of possible such axiomatisations, all based on the notion of *-autonomous category. We will particularly focus on the medial map, which has its origin in an inference rule in KS, a cut-free deductive system for Boolean logic in the calculus of structures. Finally, we will present a category of proof nets as a particularly well-behaved example of a Boolean category.
Analysis of loss networks with routing
Venue: arXiv cs.NI 2007
Year: 2007

This paper analyzes stochastic networks consisting of finite capacity nodes with different classes of requests which move according to some routing policy. The Markov processes describing these networks do not, in general, have reversibility properties, so the explicit expression of their invariant distribution is not known. Kelly's limiting regime is considered: the arrival rates of calls as well as the capacities of the nodes are proportional to a factor going to infinity. It is proved that, in limit, the associated rescaled Markov process converges to a deterministic dynamical system with a unique equilibrium point characterized by a nonstandard fixed point equation.
Why neighbor-joining works
Venue: arXiv cs.DS 2007
Year: 2007

We show that the neighbor-joining algorithm is a robust quartet method for constructing trees from distances. This leads to a new performance guarantee that contains Atteson's optimal radius bound as a special case and explains many cases where neighbor-joining is successful even when Atteson's criterion is not satisfied. We also provide a proof for Atteson's conjecture on the optimal edge radius of the neighbor-joining algorithm. The strong performance guarantees we provide also hold for the quadratic time fast neighbor-joining algorithm, thus providing a theoretical basis for inferring very large phylogenies with neighbor-joining.
Golden Space-Time Trellis Coded Modulation
Venue: arXiv cs.IT 2007
Year: 2007

In this paper, we present a concatenated coding scheme for a high rate $2\times 2$ multiple-input multiple-output (MIMO) system over slow fading channels. The inner code is the Golden code \cite{Golden05} and the outer code is a trellis code. Set partitioning of the Golden code is designed specifically to increase the minimum determinant. The branches of the outer trellis code are labeled with these partitions. Viterbi algorithm is applied for trellis decoding. In order to compute the branch metrics a lattice sphere decoder is used. The general framework for code optimization is given. The performance of the proposed concatenated scheme is evaluated by simulation. It is shown that the proposed scheme achieves significant performance gains over uncoded Golden code.
Inapproximability of the Tutte polynomial
Venue: arXiv cs.CC 2007
Year: 2007

The Tutte polynomial of a graph G is a two-variable polynomial T(G;x,y) that encodes many interesting properties of the graph. We study the complexity of the following problem, for rationals x and y: take as input a graph G, and output a value which is a good approximation to T(G;x,y). Jaeger, Vertigan and Welsh have completely mapped the complexity of exactly computing the Tutte polynomial. They have shown that this is #P-hard, except along the hyperbola (x-1)(y-1)=1 and at four special points. We are interested in determining for which points (x,y) there is a "fully polynomial randomised approximation scheme" (FPRAS) for T(G;x,y). Under the assumption RP is not equal to NP, we prove that there is no FPRAS at (x,y) if (x,y) is in one of the half-planes x<-1 or y<-1 (excluding the easy-to-compute cases mentioned above). Two exceptions to this result are the half-line x<-1, y=1 (which is still open) and the portion of the hyperbola (x-1)(y-1)=2 corresponding to y<-1 which we show to be equivalent in difficulty to approximately counting perfect matchings. We give further intractability results for (x,y) in the vicinity of the origin. A corollary of our results is that, under the assumption RP is not equal to NP, there is no FPRAS at the point (x,y)=(0,1--lambda) when λ>2 is a positive integer. Thus there is no FPRAS for counting nowhere-zero λflows for λ>2. This is an interesting consequence of our work since the corresponding decision problem is in P for example for λ=6.
An Improved Sphere-Packing Bound for Finite-Length Codes on Symmetric Memoryless Channels
Venue: arXiv cs.IT 2007
Year: 2007

This paper derives an improved sphere-packing (ISP) bound for finite-length codes whose transmission takes place over symmetric memoryless channels. We first review classical results, i.e., the 1959 sphere-packing (SP59) bound of Shannon for the Gaussian channel, and the 1967 sphere-packing (SP67) bound of Shannon et al. for discrete memoryless channels. A recent improvement on the SP67 bound, as suggested by Valembois and Fossorier, is also discussed. These concepts are used for the derivation of a new lower bound on the decoding error probability (referred to as the ISP bound) which is uniformly tighter than the SP67 bound and its recent improved version. The ISP bound is applicable to symmetric memoryless channels, and some of its applications are exemplified. Its tightness is studied by comparing it with bounds on the ML decoding error probability, and computer simulations of iteratively decoded turbo-like codes. The paper also presents a technique which performs the entire calculation of the SP59 bound in the logarithmic domain, thus facilitating the exact calculation of this bound for moderate to large block lengths without the need for the asymptotic approximations provided by Shannon.
Oblivious-Transfer Amplification
Venue: arXiv cs.CR 2007
Year: 2007

Oblivious transfer is a primitive of paramount importance in cryptography or, more precisely, two- and multi-party computation due to its universality. Unfortunately, oblivious transfer cannot be achieved in an unconditionally secure way for both parties from scratch. Therefore, it is a natural question what information-theoretic primitives or computational assumptions oblivious transfer can be based on. The results in our thesis are threefold. First, we present a protocol that implements oblivious transfer from a weakened oblivious transfer called universal oblivious transfer, where one of the two players may get additional information. Our reduction is about twice as efficient as previous results. Weak oblivious transfer is an even weaker form of oblivious transfer, where both players may obtain additional information about the other player's input, and where the output can contain errors. We give a new, weaker definition of weak oblivious transfer, as well as new reductions with a more detailed analysis. Finally, we carry over our results to the computational setting and show how a weak oblivious transfer that is sometimes incorrect and only mildly secure against computationally bounded adversaries can be strengthened.
A kernel method for canonical correlation analysis
Venue: arXiv cs.LG 2007
Year: 2007

Canonical correlation analysis is a technique to extract common features from a pair of multivariate data. In complex situations, however, it does not extract useful features because of its linearity. On the other hand, kernel method used in support vector machine is an efficient approach to improve such a linear method. In this paper, we investigate the effectiveness of applying kernel method to canonical correlation analysis.
Free Choice Petri Nets without frozen tokens and Bipolar Synchronization Systems
Venue: arXiv cs.LO 2007
Year: 2007

Bipolar synchronization systems (BP-systems) constitute a class of coloured Petri nets, well suited for modeling the control flow of discrete, dynamical systems. Every BP-system has an underlying ordinary Petri net, which is a T-system. Moreover, it has a second ordinary net attached, which is a free-choice system. We prove that a BP-system is live and safe if the T-system and the free-choice system are live and safe and if the free-choice system has no frozen tokens. This result is the converse of a theorem of Genrich and Thiagarajan and proves an elder conjecture. The proof compares the different Petri nets by Petri net morphisms and makes use of the classical theory of free-choice systems
Identifying Crosscutting Concerns Using Fan-in Analysis
Venue: arXiv cs.SE 2007
Year: 2007

Aspect mining is a reverse engineering process that aims at finding crosscutting concerns in existing systems. This paper proposes an aspect mining approach based on determining methods that are called from many different places, and hence have a high fan-in, which can be seen as a symptom of crosscutting functionality. The approach is semi-automatic, and consists of three steps: metric calculation, method filtering, and call site analysis. Carrying out these steps is an interactive process supported by an Eclipse plug-in called FINT. Fan-in analysis has been applied to three open source Java systems, totaling around 200,000 lines of code. The most interesting concerns identified are discussed in detail, which includes several concerns not previously discussed in the aspect-oriented literature. The results show that a significant number of crosscutting concerns can be recognized using fan-in analysis, and each of the three steps can be supported by tools.
Semantic results for ontic and epistemic change
Venue: arXiv cs.LO 2007
Year: 2007

We give some semantic results for an epistemic logic incorporating dynamic operators to describe information changing events. Such events include epistemic changes, where agents become more informed about the non-changing state of the world, and ontic changes, wherein the world changes. The events are executed in information states that are modeled as pointed Kripke models. Our contribution consists of three semantic results. (i) Given two information states, there is an event transforming one into the other. The linguistic correspondent to this is that every consistent formula can be made true in every information state by the execution of an event. (ii) A more technical result is that: every event corresponds to an event in which the postconditions formalizing ontic change are assignments to `true' and `false' only (instead of assignments to arbitrary formulas in the logical language). `Corresponds' means that execution of either event in a given information state results in bisimilar information states. (iii) The third, also technical, result is that every event corresponds to a sequence of events wherein all postconditions are assignments of a single atom only (instead of simultaneous assignments of more than one atom).
How To Break Anonymity of the Netflix Prize Dataset
Venue: arXiv cs.CR 2007
Year: 2007

We present a new class of statistical de-anonymization attacks against high-dimensional micro-data, such as individual preferences, recommendations, transaction records and so on. Our techniques are robust to perturbation in the data and tolerate some mistakes in the adversary's background knowledge. We apply our de-anonymization methodology to the Netflix Prize dataset, which contains anonymous movie ratings of 500,000 subscribers of Netflix, the world's largest online movie rental service. We demonstrate that an adversary who knows only a little bit about an individual subscriber can easily identify this subscriber's record in the dataset. Using the Internet Movie Database as the source of background knowledge, we successfully identified the Netflix records of known users, uncovering their apparent political preferences and other potentially sensitive information.
Local approximate inference algorithms
Venue: arXiv cs.AI 2007
Year: 2007

We present a new local approximation algorithm for computing Maximum a Posteriori (MAP) and log-partition function for arbitrary exponential family distribution represented by a finite-valued pair-wise Markov random field (MRF), say $G$. Our algorithm is based on decomposition of $G$ into {\em appropriately} chosen small components; then computing estimates locally in each of these components and then producing a {\em good} global solution. We show that if the underlying graph $G$ either excludes some finite-sized graph as its minor (e.g. Planar graph) or has low doubling dimension (e.g. any graph with {\em geometry}), then our algorithm will produce solution for both questions within {\em arbitrary accuracy}. We present a message-passing implementation of our algorithm for MAP computation using self-avoiding walk of graph. In order to evaluate the computational cost of this implementation, we derive novel tight bounds on the size of self-avoiding walk tree for arbitrary graph. As a consequence of our algorithmic result, we show that the normalized log-partition function (also known as free-energy) for a class of {\em regular} MRFs will converge to a limit, that is computable to an arbitrary accuracy.
Source coding and channel requirements for unstable processes
Venue: arXiv cs.IT 2007
Year: 2007

Our understanding of information in systems has been based on the foundation of memoryless processes. Extensions to stable Markov and auto-regressive processes are classical. Berger proved a source coding theorem for the marginally unstable Wiener process, but the infinite-horizon exponentially unstable case has been open since Gray's 1970 paper. There were also no theorems showing what is needed to communicate such processes across noisy channels. In this work, we give a fixed-rate source-coding theorem for the infinite-horizon problem of coding an exponentially unstable Markov process. The encoding naturally results in two distinct bitstreams that have qualitatively different QoS requirements for communicating over a noisy medium. The first stream captures the information that is accumulating within the nonstationary process and requires sufficient anytime reliability from the channel used to communicate the process. The second stream captures the historical information that dissipates within the process and is essentially classical. This historical information can also be identified with a natural stable counterpart to the unstable process. A converse demonstrating the fundamentally layered nature of unstable sources is given by means of information-embedding ideas.
Algorithmic Aspects of a General Modular Decomposition Theory
Venue: arXiv cs.DS 2007
Year: 2007

A new general decomposition theory inspired from modular graph decomposition is presented. This helps unifying modular decomposition on different structures, including (but not restricted to) graphs. Moreover, even in the case of graphs, the terminology ``module'' not only captures the classical graph modules but also allows to handle 2-connected components, star-cutsets, and other vertex subsets. The main result is that most of the nice algorithmic tools developed for modular decomposition of graphs still apply efficiently on our generalisation of modules. Besides, when an essential axiom is satisfied, almost all the important properties can be retrieved. For this case, an algorithm given by Ehrenfeucht, Gabow, McConnell and Sullivan 1994 is generalised and yields a very efficient solution to the associated decomposition problem.
A Decomposition Theory for Binary Linear Codes
Venue: arXiv cs.DM 2007
Year: 2007

The decomposition theory of matroids initiated by Paul Seymour in the 1980's has had an enormous impact on research in matroid theory. This theory, when applied to matrices over the binary field, yields a powerful decomposition theory for binary linear codes. In this paper, we give an overview of this code decomposition theory, and discuss some of its implications in the context of the recently discovered formulation of maximum-likelihood (ML) decoding of a binary linear code over a discrete memoryless channel as a linear programming problem. We translate matroid-theoretic results of Grötschel and Truemper from the combinatorial optimization literature to give examples of non-trivial families of codes for which the ML decoding problem can be solved in time polynomial in the length of the code. One such family is that consisting of codes $C$ for which the codeword polytope is identical to the Koetter-Vontobel fundamental polytope derived from the entire dual code $C^\perp$. However, we also show that such families of codes are not good in a coding-theoretic sense -- either their dimension or their minimum distance must grow sub-linearly with codelength. As a consequence, we have that decoding by linear programming, when applied to good codes, cannot avoid failing occasionally due to the presence of pseudocodewords.
V-like formations in flocks of artificial birds
Venue: arXiv cs.NE 2007
Year: 2007

We consider flocks of artificial birds and study the emergence of V-like formations during flight. We introduce a small set of fully distributed positioning rules to guide the birds' movements and demonstrate, by means of simulations, that they tend to lead to stabilization into several of the well-known V-like formations that have been observed in nature. We also provide quantitative indicators that we believe are closely related to achieving V-like formations, and study their behavior over a large set of independent simulations.
Hierarchical Cooperation Achieves Optimal Capacity Scaling in Ad Hoc Networks
Venue: arXiv cs.IT 2007
Year: 2007

n source and destination pairs randomly located in an area want to communicate with each other. Signals transmitted from one user to another at distance r apart are subject to a power loss of r^{-alpha}, as well as a random phase. We identify the scaling laws of the information theoretic capacity of the network. In the case of dense networks, where the area is fixed and the density of nodes increasing, we show that the total capacity of the network scales linearly with n. This improves on the best known achievability result of n^{2/3} of Aeron and Saligrama, 2006. In the case of extended networks, where the density of nodes is fixed and the area increasing linearly with n, we show that this capacity scales as n^{2-alpha/2} for 2<alpha<3 and sqrt{n} for alpha>3. The best known earlier result (Xie and Kumar 2006) identified the scaling law for alpha > 4. Thus, much better scaling than multihop can be achieved in dense networks, as well as in extended networks with low attenuation. The performance gain is achieved by intelligent node cooperation and distributed MIMO communication. The key ingredient is a hierarchical and digital architecture for nodal exchange of information for realizing the cooperation.
Expressiveness of Metric modalities for continuous time
Venue: arXiv cs.LO 2007
Year: 2007

We prove a conjecture by A. Pnueli and strengthen it showing a sequence of "counting modalities" none of which is expressible in the temporal logic generated by the previous modalities, over the real line, or over the positive reals. Moreover, there is no finite temporal logic that can express all of them over the real line, so that no finite metric temporal logic is expressively complete.